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PDBsum entry 1peg

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1peg
Jmol
Contents
Protein chains
266 a.a. *
Ligands
ALA-ARG-LYS-SER-
THR-GLY-GLY
ALA-ARG-LYS-SER-
THR
SAH ×2
Metals
_ZN ×8
* Residue conservation analysis
PDB id:
1peg
Name: Transferase
Title: Structural basis for the product specificity of histone lysine methyltransferases
Structure: Histone h3 methyltransferase dim-5. Chain: a, b. Fragment: residues 17-318. Engineered: yes. Histone h3. Chain: p, q. Fragment: residues 1-15. Engineered: yes
Source: Neurospora crassa. Organism_taxid: 5141. Expressed in: escherichia coli. Expression_system_taxid: 562. (Stratagene). Synthetic: yes. Other_details: the histone h3 peptide (n-terminal residues 1-15) is synthesized.
Biol. unit: Dimer (from PQS)
Resolution:
2.59Å     R-factor:   0.220     R-free:   0.320
Authors: X.Zhang,Z.Yang,S.I.Khan,J.R.Horton,H.Tamaru,E.U.Selker, X.Cheng
Key ref:
X.Zhang et al. (2003). Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell, 12, 177-185. PubMed id: 12887903 DOI: 10.1016/S1097-2765(03)00224-7
Date:
21-May-03     Release date:   05-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8X225  (DIM5_NEUCR) -  Histone-lysine N-methyltransferase, H3 lysine-9 specific dim-5
Seq:
Struc:
331 a.a.
266 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.43  - Histone-lysine N-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N6-methyl-L-lysine-[histone]
S-adenosyl-L-methionine
+ L-lysine-[histone]
=
S-adenosyl-L-homocysteine
Bound ligand (Het Group name = SAH)
corresponds exactly
+ N(6)-methyl-L-lysine-[histone]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   2 terms 
  Biological process     methylation   2 terms 
  Biochemical function     protein binding     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S1097-2765(03)00224-7 Mol Cell 12:177-185 (2003)
PubMed id: 12887903  
 
 
Structural basis for the product specificity of histone lysine methyltransferases.
X.Zhang, Z.Yang, S.I.Khan, J.R.Horton, H.Tamaru, E.U.Selker, X.Cheng.
 
  ABSTRACT  
 
DIM-5 is a SUV39-type histone H3 Lys9 methyltransferase that is essential for DNA methylation in N. crassa. We report the structure of a ternary complex including DIM-5, S-adenosyl-L-homocysteine, and a substrate H3 peptide. The histone tail inserts as a parallel strand between two DIM-5 strands, completing a hybrid sheet. Three post-SET cysteines coordinate a zinc atom together with Cys242 from the SET signature motif (NHXCXPN) near the active site. Consequently, a narrow channel is formed to accommodate the target Lys9 side chain. The sulfur atom of S-adenosyl-L-homocysteine, where the transferable methyl group is to be attached in S-adenosyl-L-methionine, lies at the opposite end of the channel, approximately 4 A away from the target Lys9 nitrogen. Structural comparison of the active sites of DIM-5, an H3 Lys9 trimethyltransferase, and SET7/9, an H3 Lys4 monomethyltransferase, allowed us to design substitutions in both enzymes that profoundly alter their product specificities without affecting their catalytic activities.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. DIM-5 Kinetics and Ternary Structure(A) Mass spectrometry analysis of different H3 peptides as DIM-5 substrates. The relative amount of each peptide species, expressed as a percentage of the sum of intensity of all related peaks, was plotted over the full time courses of the reactions.(B) GRASP (Nicholls et al., 1991) surface charge distribution (blue for positive, red for negative, white for neutral). The H3 peptide and AdoHcy are shown as stick models.(C) Ribbon (Carson, 1997) diagram colored as in Figure 1. The pre-SET residues (yellow) form a Zn[3]Cys[9] triangular zinc cluster. The SET residues (green) and the N-terminal region are folded into six β sheets surrounding a knot-like structure (magenta). The post-SET residues (gray) bind the fourth zinc atom, adjacent to the substrate H3 peptide (red) and AdoHcy (blue).(D) The substrate H3 peptide (red), superimposed on an omit electron density contoured at 4.0 σ (orange), is inserted as a parallel β strand (red in Figure 2C) between two DIM-5 strands, β10 (green) and β18 (magenta). The side chain density for H3 Arg-8 is complete at lower contour levels (2.5 σ in F[obs]-F[cal] and 0.8 σ in 2F[obs]-F[cal]).
Figure 3.
Figure 3. The Methylation Mechanism(A) The post-SET zinc ion and the AdoHcy binding site. The zinc ion is presented as a red ball, coordinated by four cysteines, C244 (magenta) and C^306XC^308X[4]C^313 (gray). AdoHcy is superimposed onto a difference electron density map contoured at 4.0 σ (orange). Dashed lines indicate the hydrogen bonds. One face of the AdoHcy adenine base lies against the aliphatic portion of R159, whose guanidino group forms a bifurcated salt bridge with the two carboxyl oxygen atoms of E278. The polar edge of the adenine base forms three hydrogen bonds to the DIM-5 backbone: the exocyclic amino group N6 with the carbonyl oxygen of H242, the ring N1 with the amide of L307, and the ring N7 with the amide of H242. The adenine ring carbon C8 makes van der Waals contacts to the Y283 hydroxyl and with the side chain carbonyl Oδ1 of N241; this explains the complete loss of AdoMet crosslinking in N241Q and Y283F mutants (Zhang et al., 2002). The two ribose hydroxyls interact with the main chain amide of V203 and the side chain carboxyl of D202. The amino group of the homocysteine moiety hydrogen bonds the side chain Oδ1 of N241, while its side chain amino group forms two hydrogen bonds with the backbone carbonyl of W161 and with the side chain of E278. The carboxylate group of the homocysteine moiety interacts with Y204 and the backbone amide of W161.(B) Close-up view of the H3 peptide binding site with Lys9 inserted into a channel.(C) The target Lys binding site (stereo). The arrow indicates the movement of the methyl group transferred from the AdoMet methylsulfonium group to the target amino group.(D) DIM-5 activity (LogCPM) as a function of pH.(E) AdoHcy bound in a large surface pocket, allowing for processive methylation. The green ellipse indicates the location where the AdoHcy homocysteine moiety binds in the peptide-free structure (Zhang et al., 2002).
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 12, 177-185) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21276944 A.Dhayalan, S.Kudithipudi, P.Rathert, and A.Jeltsch (2011).
Specificity analysis-based identification of new methylation targets of the SET7/9 protein lysine methyltransferase.
  Chem Biol, 18, 111-120.  
21321607 A.J.Bannister, and T.Kouzarides (2011).
Regulation of chromatin by histone modifications.
  Cell Res, 21, 381-395.  
  21141727 A.K.Upadhyay, and X.Cheng (2011).
Dynamics of histone lysine methylation: structures of methyl writers and erasers.
  Prog Drug Res, 67, 107-124.  
21190999 D.B.Yap, J.Chu, T.Berg, M.Schapira, S.W.Cheng, A.Moradian, R.D.Morin, A.J.Mungall, B.Meissner, M.Boyle, V.E.Marquez, M.A.Marra, R.D.Gascoyne, R.K.Humphries, C.H.Arrowsmith, G.B.Morin, and S.A.Aparicio (2011).
Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation.
  Blood, 117, 2451-2459.  
21243713 S.Krishnan, S.Horowitz, and R.C.Trievel (2011).
Structure and function of histone H3 lysine 9 methyltransferases and demethylases.
  Chembiochem, 12, 254-263.  
21220120 V.Avdic, P.Zhang, S.Lanouette, A.Groulx, V.Tremblay, J.Brunzelle, and J.F.Couture (2011).
Structural and biochemical insights into MLL1 core complex assembly.
  Structure, 19, 101-108.
PDB code: 3p4f
21124902 F.Cao, Y.Chen, T.Cierpicki, Y.Liu, V.Basrur, M.Lei, and Y.Dou (2010).
An Ash2L/RbBP5 heterodimer stimulates the MLL1 methyltransferase activity through coordinated substrate interactions with the MLL1 SET domain.
  PLoS One, 5, e14102.  
20084102 H.Wu, J.Min, V.V.Lunin, T.Antoshenko, L.Dombrovski, H.Zeng, A.Allali-Hassani, V.Campagna-Slater, M.Vedadi, C.H.Arrowsmith, A.N.Plotnikov, and M.Schapira (2010).
Structural biology of human H3K9 methyltransferases.
  PLoS One, 5, e8570.
PDB codes: 2igq 2o8j 2qpw 2r3a 2rfi 3hna
20236310 M.S.Cosgrove, and A.Patel (2010).
Mixed lineage leukemia: a structure-function perspective of the MLL1 protein.
  FEBS J, 277, 1832-1842.  
20024091 R.H.Cichewicz (2010).
Epigenome manipulation as a pathway to new natural product scaffolds and their congeners.
  Nat Prod Rep, 27, 11-22.  
21062871 T.Sahr, T.Adam, C.Fizames, C.Maurel, and V.Santoni (2010).
O-carboxyl- and N-methyltransferases active on plant aquaporins.
  Plant Cell Physiol, 51, 2092-2104.  
19556245 A.Patel, V.Dharmarajan, V.E.Vought, and M.S.Cosgrove (2009).
On the mechanism of multiple lysine methylation by the human mixed lineage leukemia protein-1 (MLL1) core complex.
  J Biol Chem, 284, 24242-24256.  
18603028 B.C.Smith, and J.M.Denu (2009).
Chemical mechanisms of histone lysine and arginine modifications.
  Biochim Biophys Acta, 1789, 45-57.  
19864627 C.K.Ea, and D.Baltimore (2009).
Regulation of NF-kappaB activity through lysine monomethylation of p65.
  Proc Natl Acad Sci U S A, 106, 18972-18977.  
  19961595 L.Colin, and C.Van Lint (2009).
Molecular control of HIV-1 postintegration latency: implications for the development of new therapeutic strategies.
  Retrovirology, 6, 111.  
19362589 M.J.Hitchler, and F.E.Domann (2009).
Metabolic defects provide a spark for the epigenetic switch in cancer.
  Free Radic Biol Med, 47, 115-127.  
19882600 Q.Xu, Y.Z.Chu, H.B.Guo, J.C.Smith, and H.Guo (2009).
Energy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferases.
  Chemistry, 15, 12596-12599.  
19721445 R.A.Copeland, M.E.Solomon, and V.M.Richon (2009).
Protein methyltransferases as a target class for drug discovery.
  Nat Rev Drug Discov, 8, 724-732.  
  19684477 S.Pradhan, H.G.Chin, P.O.Estève, and S.E.Jacobsen (2009).
SET7/9 mediated methylation of non-histone proteins in mammalian cells.
  Epigenetics, 4, 383-387.  
19208805 S.Raunser, R.Magnani, Z.Huang, R.L.Houtz, R.C.Trievel, P.A.Penczek, and T.Walz (2009).
Rubisco in complex with Rubisco large subunit methyltransferase.
  Proc Natl Acad Sci U S A, 106, 3160-3165.  
  20582239 T.Petrossian, and S.Clarke (2009).
Bioinformatic Identification of Novel Methyltransferases.
  Epigenomics, 1, 163-175.  
19219047 Y.Chang, X.Zhang, J.R.Horton, A.K.Upadhyay, A.Spannhoff, J.Liu, J.P.Snyder, M.T.Bedford, and X.Cheng (2009).
Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294.
  Nat Struct Mol Biol, 16, 312-317.
PDB code: 3fpd
19398585 Y.H.Takahashi, J.S.Lee, S.K.Swanson, A.Saraf, L.Florens, M.P.Washburn, R.C.Trievel, and A.Shilatifard (2009).
Regulation of H3K4 trimethylation via Cps40 (Spp1) of COMPASS is monoubiquitination independent: implication for a Phe/Tyr switch by the catalytic domain of Set1.
  Mol Cell Biol, 29, 3478-3486.  
18829457 A.Patel, V.E.Vought, V.Dharmarajan, and M.S.Cosgrove (2008).
A Conserved Arginine-containing Motif Crucial for the Assembly and Enzymatic Activity of the Mixed Lineage Leukemia Protein-1 Core Complex.
  J Biol Chem, 283, 32162-32175.  
18263876 B.D.Beck, S.J.Park, Y.J.Lee, Y.Roman, R.A.Hromas, and S.H.Lee (2008).
Human Pso4 is a metnase (SETMAR)-binding partner that regulates metnase function in DNA repair.
  J Biol Chem, 283, 9023-9030.  
18593478 C.S.Veerappan, Z.Avramova, and E.N.Moriyama (2008).
Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi.
  BMC Evol Biol, 8, 190.  
18511943 F.Frederiks, M.Tzouros, G.Oudgenoeg, T.van Welsem, M.Fornerod, J.Krijgsveld, and F.van Leeuwen (2008).
Nonprocessive methylation by Dot1 leads to functional redundancy of histone H3K79 methylation states.
  Nat Struct Mol Biol, 15, 550-557.  
18221488 G.Brosch, P.Loidl, and S.Graessle (2008).
Histone modifications and chromatin dynamics: a focus on filamentous fungi.
  FEMS Microbiol Rev, 32, 409-439.  
18611379 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2008).
Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase.
  Structure, 16, 1059-1066.
PDB codes: 3cjq 3cjr 3cjs 3cjt 3cju 3egv
19088188 J.F.Couture, L.M.Dirk, J.S.Brunzelle, R.L.Houtz, and R.C.Trievel (2008).
Structural origins for the product specificity of SET domain protein methyltransferases.
  Proc Natl Acad Sci U S A, 105, 20659-20664.
PDB codes: 3f9w 3f9x 3f9y 3f9z
19141471 K.K.Adhvaryu, and E.U.Selker (2008).
Protein phosphatase PP1 is required for normal DNA methylation in Neurospora.
  Genes Dev, 22, 3391-3396.  
18471979 K.Subramanian, D.Jia, P.Kapoor-Vazirani, D.R.Powell, R.E.Collins, D.Sharma, J.Peng, X.Cheng, and P.M.Vertino (2008).
Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase.
  Mol Cell, 30, 336-347.
PDB codes: 3cbm 3cbo 3cbp
18070919 L.Xu, Z.Zhao, A.Dong, L.Soubigou-Taconnat, J.P.Renou, A.Steinmetz, and W.H.Shen (2008).
Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana.
  Mol Cell Biol, 28, 1348-1360.  
18311969 P.Hu, S.Wang, and Y.Zhang (2008).
How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations.
  J Am Chem Soc, 130, 3806-3813.  
18693240 P.Joshi, E.A.Carrington, L.Wang, C.S.Ketel, E.L.Miller, R.S.Jones, and J.A.Simon (2008).
Dominant Alleles Identify SET Domain Residues Required for Histone Methyltransferase of Polycomb Repressive Complex 2.
  J Biol Chem, 283, 27757-27766.  
18215768 P.Rathert, X.Zhang, C.Freund, X.Cheng, and A.Jeltsch (2008).
Analysis of the substrate specificity of the Dim-5 histone lysine methyltransferase using peptide arrays.
  Chem Biol, 15, 5.  
17710556 V.Krauss (2008).
Glimpses of evolution: heterochromatic histone H3K9 methyltransferases left its marks behind.
  Genetica, 133, 93.  
18391193 X.Zhang, and T.C.Bruice (2008).
Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases.
  Proc Natl Acad Sci U S A, 105, 5728-5732.  
18650421 Y.Li, M.A.Reddy, F.Miao, N.Shanmugam, J.K.Yee, D.Hawkins, B.Ren, and R.Natarajan (2008).
Role of the histone H3 lysine 4 methyltransferase, SET7/9, in the regulation of NF-kappaB-dependent inflammatory genes. Relevance to diabetes and inflammation.
  J Biol Chem, 283, 26771-26781.  
17562855 C.F.Sautel, D.Cannella, O.Bastien, S.Kieffer, D.Aldebert, J.Garin, I.Tardieux, H.Belrhali, and M.A.Hakimi (2007).
SET8-mediated methylations of histone H4 lysine 20 mark silent heterochromatic domains in apicomplexan genomes.
  Mol Cell Biol, 27, 5711-5724.  
17517655 H.B.Guo, and H.Guo (2007).
Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity.
  Proc Natl Acad Sci U S A, 104, 8797-8802.  
17215866 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2007).
Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA.
  EMBO J, 26, 567-577.
PDB codes: 2nxc 2nxe 2nxj 2nxn
17251191 J.A.Casas-Mollano, K.van Dijk, J.Eisenhart, and H.Cerutti (2007).
SET3p monomethylates histone H3 on lysine 9 and is required for the silencing of tandemly repeated transgenes in Chlamydomonas.
  Nucleic Acids Res, 35, 939-950.  
17934479 K.L.Rice, I.Hormaeche, and J.D.Licht (2007).
Epigenetic regulation of normal and malignant hematopoiesis.
  Oncogene, 26, 6697-6714.  
17761298 M.J.Hitchler, and F.E.Domann (2007).
An epigenetic perspective on the free radical theory of development.
  Free Radic Biol Med, 43, 1023-1036.  
17529991 M.Yang, J.C.Culhane, L.M.Szewczuk, C.B.Gocke, C.A.Brautigam, D.R.Tomchick, M.Machius, P.A.Cole, and H.Yu (2007).
Structural basis of histone demethylation by LSD1 revealed by suicide inactivation.
  Nat Struct Mol Biol, 14, 535-539.
PDB code: 2uxn
  18072589 P.Rathert, X.Cheng, and A.Jeltsch (2007).
Continuous enzymatic assay for histone lysine methyltransferases.
  Biotechniques, 43, 602, 604, 606 passim.  
17289593 S.Kubicek, R.J.O'Sullivan, E.M.August, E.R.Hickey, Q.Zhang, M.L.Teodoro, S.Rea, K.Mechtler, J.A.Kowalski, C.A.Homon, T.A.Kelly, and T.Jenuwein (2007).
Reversal of H3K9me2 by a small-molecule inhibitor for the G9a histone methyltransferase.
  Mol Cell, 25, 473-481.  
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
17388541 S.Wang, P.Hu, and Y.Zhang (2007).
Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.
  J Phys Chem B, 111, 3758-3764.  
17960915 T.C.Osborne, O.Obianyo, X.Zhang, X.Cheng, and P.R.Thompson (2007).
Protein arginine methyltransferase 1: positively charged residues in substrate peptides distal to the site of methylation are important for substrate binding and catalysis.
  Biochemistry, 46, 13370-13381.  
17374386 X.Cheng, and X.Zhang (2007).
Structural dynamics of protein lysine methylation and demethylation.
  Mutat Res, 618, 102-115.  
17567753 Z.Chen, J.Zang, J.Kappler, X.Hong, F.Crawford, Q.Wang, F.Lan, C.Jiang, J.Whetstine, S.Dai, K.Hansen, Y.Shi, and G.Zhang (2007).
Structural basis of the recognition of a methylated histone tail by JMJD2A.
  Proc Natl Acad Sci U S A, 104, 10818-10823.
PDB codes: 2p5b 2pxj
16829959 A.J.Ruthenburg, W.Wang, D.M.Graybosch, H.Li, C.D.Allis, D.J.Patel, and G.L.Verdine (2006).
Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex.
  Nat Struct Mol Biol, 13, 704-712.
PDB codes: 2cnx 2co0 2h68 2h6k 2h6n 2h6q
16738407 B.D.Fodor, S.Kubicek, M.Yonezawa, R.J.O'Sullivan, R.Sengupta, L.Perez-Burgos, S.Opravil, K.Mechtler, G.Schotta, and T.Jenuwein (2006).
Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells.
  Genes Dev, 20, 1557-1562.  
16415881 J.F.Couture, E.Collazo, G.Hauk, and R.C.Trievel (2006).
Structural basis for the methylation site specificity of SET7/9.
  Nat Struct Mol Biol, 13, 140-146.
PDB code: 2f69
16682405 J.F.Couture, G.Hauk, M.J.Thompson, G.M.Blackburn, and R.C.Trievel (2006).
Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases.
  J Biol Chem, 281, 19280-19287.
PDB codes: 2h21 2h23 2h2e 2h2j
17070031 J.F.Couture, and R.C.Trievel (2006).
Histone-modifying enzymes: encrypting an enigmatic epigenetic code.
  Curr Opin Struct Biol, 16, 753-760.  
16622709 J.Mis, S.S.Ner, and T.A.Grigliatti (2006).
Identification of three histone methyltransferases in Drosophila: dG9a is a suppressor of PEV and is required for gene silencing.
  Mol Genet Genomics, 275, 513-526.  
17362353 M.Stabell, M.Bjørkmo, R.B.Aalen, and A.Lambertsson (2006).
The Drosophila SET domain encoding gene dEset is essential for proper development.
  Hereditas, 143, 177-188.  
16963494 M.Stabell, R.Eskeland, M.Bjørkmo, J.Larsson, R.B.Aalen, A.Imhof, and A.Lambertsson (2006).
The Drosophila G9a gene encodes a multi-catalytic histone methyltransferase required for normal development.
  Nucleic Acids Res, 34, 4609-4621.  
16857008 T.Jenuwein (2006).
The epigenetic magic of histone lysine methylation.
  FEBS J, 273, 3121-3135.  
17020925 T.Thorstensen, A.Fischer, S.V.Sandvik, S.S.Johnsen, P.E.Grini, G.Reuter, and R.B.Aalen (2006).
The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9.
  Nucleic Acids Res, 34, 5461-5470.  
16512904 V.Krauss, A.Fassl, P.Fiebig, I.Patties, and H.Sass (2006).
The evolution of the histone methyltransferase gene Su(var)3-9 in metazoans includes a fusion with and a re-fission from a functionally unrelated gene.
  BMC Evol Biol, 6, 18.  
16362057 Y.Tsukada, J.Fang, H.Erdjument-Bromage, M.E.Warren, C.H.Borchers, P.Tempst, and Y.Zhang (2006).
Histone demethylation by a family of JmjC domain-containing proteins.
  Nature, 439, 811-816.  
16677698 Z.Chen, J.Zang, J.Whetstine, X.Hong, F.Davrazou, T.G.Kutateladze, M.Simpson, Q.Mao, C.H.Pan, S.Dai, J.Hagman, K.Hansen, Y.Shi, and G.Zhang (2006).
Structural insights into histone demethylation by JMJD2 family members.
  Cell, 125, 691-702.
PDB codes: 2gp3 2gp5
15933069 B.Xiao, C.Jing, G.Kelly, P.A.Walker, F.W.Muskett, T.A.Frenkiel, S.R.Martin, K.Sarma, D.Reinberg, S.J.Gamblin, and J.R.Wilson (2005).
Specificity and mechanism of the histone methyltransferase Pr-Set7.
  Genes Dev, 19, 1444-1454.
PDB code: 2bqz
15822187 D.C.Drummond, C.O.Noble, D.B.Kirpotin, Z.Guo, G.K.Scott, and C.C.Benz (2005).
Clinical development of histone deacetylase inhibitors as anticancer agents.
  Annu Rev Pharmacol Toxicol, 45, 495-528.  
15935324 H.Gowher, X.Zhang, X.Cheng, and A.Jeltsch (2005).
Avidin plate assay system for enzymatic characterization of a histone lysine methyltransferase.
  Anal Biochem, 342, 287-291.  
15964832 I.M.Fingerman, C.L.Wu, B.D.Wilson, and S.D.Briggs (2005).
Global loss of Set1-mediated H3 Lys4 trimethylation is associated with silencing defects in Saccharomyces cerevisiae.
  J Biol Chem, 280, 28761-28765.  
15933070 J.F.Couture, E.Collazo, J.S.Brunzelle, and R.C.Trievel (2005).
Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase.
  Genes Dev, 19, 1455-1465.
PDB code: 1zkk
16087750 K.K.Adhvaryu, S.A.Morris, B.D.Strahl, and E.U.Selker (2005).
Methylation of histone H3 lysine 36 is required for normal development in Neurospora crassa.
  Eukaryot Cell, 4, 1455-1464.  
16039595 M.D.Shahbazian, K.Zhang, and M.Grunstein (2005).
Histone H2B ubiquitylation controls processive methylation but not monomethylation by Dot1 and Set1.
  Mol Cell, 19, 271-277.  
15797202 M.Freitag, and E.U.Selker (2005).
Controlling DNA methylation: many roads to one modification.
  Curr Opin Genet Dev, 15, 191-199.  
15939934 P.O.Estève, D.Patnaik, H.G.Chin, J.Benner, M.A.Teitell, and S.Pradhan (2005).
Functional analysis of the N- and C-terminus of mammalian G9a histone H3 methyltransferase.
  Nucleic Acids Res, 33, 3211-3223.  
15590646 R.E.Collins, M.Tachibana, H.Tamaru, K.M.Smith, D.Jia, X.Zhang, E.U.Selker, Y.Shinkai, and X.Cheng (2005).
In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases.
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15788566 R.Wu, A.V.Terry, P.B.Singh, and D.M.Gilbert (2005).
Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states.
  Mol Biol Cell, 16, 2872-2881.  
16086857 S.C.Dillon, X.Zhang, R.C.Trievel, and X.Cheng (2005).
The SET-domain protein superfamily: protein lysine methyltransferases.
  Genome Biol, 6, 227.  
16332963 S.H.Lee, M.Oshige, S.T.Durant, K.K.Rasila, E.A.Williamson, H.Ramsey, L.Kwan, J.A.Nickoloff, and R.Hromas (2005).
The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair.
  Proc Natl Acad Sci U S A, 102, 18075-18080.  
15869391 X.Cheng, R.E.Collins, and X.Zhang (2005).
Structural and sequence motifs of protein (histone) methylation enzymes.
  Annu Rev Biophys Biomol Struct, 34, 267-294.  
15964846 Y.Yin, C.Liu, S.N.Tsai, B.Zhou, S.M.Ngai, and G.Zhu (2005).
SET8 recognizes the sequence RHRK20VLRDN within the N terminus of histone H4 and mono-methylates lysine 20.
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15182349 A.E.Ehrenhofer-Murray (2004).
Chromatin dynamics at DNA replication, transcription and repair.
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  15597739 D.J.Ebbole, Y.Jin, M.Thon, H.Pan, E.Bhattarai, T.Thomas, and R.Dean (2004).
Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: analysis of expressed sequence tags.
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15485804 D.Patnaik, H.G.Chin, P.O.Estève, J.Benner, S.E.Jacobsen, and S.Pradhan (2004).
Substrate specificity and kinetic mechanism of mammalian G9a histone H3 methyltransferase.
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15292170 K.Sawada, Z.Yang, J.R.Horton, R.E.Collins, X.Zhang, and X.Cheng (2004).
Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase.
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PDB code: 1u2z
15146494 L.M.Iyer, and L.Aravind (2004).
The emergence of catalytic and structural diversity within the beta-clip fold.
  Proteins, 55, 977-991.  
14967149 M.Freitag, P.C.Hickey, T.K.Khlafallah, N.D.Read, and E.U.Selker (2004).
HP1 is essential for DNA methylation in neurospora.
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15184976 M.J.Bottomley (2004).
Structures of protein domains that create or recognize histone modifications.
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16117651 M.Lachner, R.Sengupta, G.Schotta, and T.Jenuwein (2004).
Trilogies of histone lysine methylation as epigenetic landmarks of the eukaryotic genome.
  Cold Spring Harb Symp Quant Biol, 69, 209-218.  
15659850 Z.Zhao, and W.H.Shen (2004).
Plants contain a high number of proteins showing sequence similarity to the animal SUV39H family of histone methyltransferases.
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14690609 A.H.Peters, S.Kubicek, K.Mechtler, R.J.O'Sullivan, A.A.Derijck, L.Perez-Burgos, A.Kohlmaier, S.Opravil, M.Tachibana, Y.Shinkai, J.H.Martens, and T.Jenuwein (2003).
Partitioning and plasticity of repressive histone methylation states in mammalian chromatin.
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14675547 B.Xiao, J.R.Wilson, and S.J.Gamblin (2003).
SET domains and histone methylation.
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12887887 R.N.Dutnall (2003).
Cracking the histone code: one, two, three methyls, you're out!
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